Perhaps it'd be better to have an environment variable set in Xcode defining whether you want to compile user libraries or not, would be much easier than changing a list in the makefile. You could have the envar as a list of user librares too.

There are people attempting to unravel the template format (why Apple had to change it in Xcode 4 to this weird new system we'll never know) for coding other projects too. You aren't alone in trying to decipher it, but only asking for help via the Arduino on Xcode project means the audience is pretty small. I'm sure someone will figure it out (or it'll get leaked from Apple) sometime.

You're right that Xcode is really designed for OS X and iOS, Apple has little interest in supporting other languages/platforms. Despite its limitations though, I'd personally rather use Xcode. NetBeans is Java, which is usually pretty clunky and un Mac-like. I don't have experience with anything but the Arduino IDE, and Xcode on the Mac however.